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Wong J, Yellamaty R, Gallante C, Lawrence E, Martelly W, Sharma S. Examining the capacity of human U1 snRNA variants to facilitate pre-mRNA splicing. RNA (NEW YORK, N.Y.) 2024; 30:271-280. [PMID: 38164604 PMCID: PMC10870369 DOI: 10.1261/rna.079892.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
The human U1 snRNA is encoded by a multigene family consisting of transcribed variants and defective pseudogenes. Many variant U1 (vU1) snRNAs have been demonstrated to not only be transcribed but also processed by the addition of a trimethylated guanosine cap, packaged into snRNPs, and assembled into spliceosomes; however, their capacity to facilitate pre-mRNA splicing has, so far, not been tested. A recent systematic analysis of the human snRNA genes identified 178 U1 snRNA genes that are present in the genome as either tandem arrays or single genes on multiple chromosomes. Of these, 15 were found to be expressed in human tissues and cell lines, although at significantly low levels from their endogenous loci, <0.001% of the canonical U1 snRNA. In this study, we found that placing the variants in the context of the regulatory elements of the RNU1-1 gene improves the expression of many variants to levels comparable to the canonical U1 snRNA. Application of a previously established HeLa cell-based minigene reporter assay to examine the capacity of the vU1 snRNAs to support pre-mRNA splicing revealed that even though the exogenously expressed variant snRNAs were enriched in the nucleus, only a few had a measurable effect on splicing.
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Affiliation(s)
- Jason Wong
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - Ryan Yellamaty
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - Christina Gallante
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - Ethan Lawrence
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - William Martelly
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - Shalini Sharma
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
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2
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Gonçalves M, Santos JI, Coutinho MF, Matos L, Alves S. Development of Engineered-U1 snRNA Therapies: Current Status. Int J Mol Sci 2023; 24:14617. [PMID: 37834063 PMCID: PMC10572768 DOI: 10.3390/ijms241914617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Splicing of pre-mRNA is a crucial regulatory stage in the pathway of gene expression. The majority of human genes that encode proteins undergo alternative pre-mRNA splicing and mutations that affect splicing are more prevalent than previously thought. Targeting aberrant RNA(s) may thus provide an opportunity to correct faulty splicing and potentially treat numerous genetic disorders. To that purpose, the use of engineered U1 snRNA (either modified U1 snRNAs or exon-specific U1s-ExSpeU1s) has been applied as a potentially therapeutic strategy to correct splicing mutations, particularly those affecting the 5' splice-site (5'ss). Here we review and summarize a vast panoply of studies that used either modified U1 snRNAs or ExSpeU1s to mediate gene therapeutic correction of splicing defects underlying a considerable number of genetic diseases. We also focus on the pre-clinical validation of these therapeutic approaches both in vitro and in vivo, and summarize the main obstacles that need to be overcome to allow for their successful translation to clinic practice in the future.
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Affiliation(s)
- Mariana Gonçalves
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, CITAB, Inov4Agro, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - Juliana Inês Santos
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Maria Francisca Coutinho
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Liliana Matos
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Sandra Alves
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
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3
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Mo Z, Li R, Cao C, Li Y, Zheng S, Wu R, Xue J, Hu J, Meng H, Zhai H, Huang W, Zheng F, Zhou B. Splicing factor SNRPA associated with microvascular invasion promotes hepatocellular carcinoma metastasis through activating NOTCH1/Snail pathway and is mediated by circSEC62/miR-625-5p axis. ENVIRONMENTAL TOXICOLOGY 2023; 38:1022-1037. [PMID: 36715182 DOI: 10.1002/tox.23745] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 12/10/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Microvascular invasion (MVI) is a crucial risk factor related to the metastasis of hepatocellular carcinoma (HCC), but the underlying mechanisms remain to be revealed. Characterizing the inherent mechanisms of MVI may aid in the development of effective treatment strategies to improve the prognosis of HCC patients with metastasis. Through the Gene Expression Omnibus (GEO) database, we identified that small nuclear ribonucleoprotein polypeptide A (SNRPA) was related to MVI in HCC. SNRPA was overexpressed in MVI-HCC and correlated with poor patient survival. Mechanistically, SNRPA promoted the epithelial-mesenchymal transition (EMT)-like process for HCC cells to accelerate metastasis by activating the NOTCH1/Snail pathway in vitro and in vivo. Importantly, circSEC62 upregulated SNRPA expression in HCC cells via miR-625-5p sponging. Taking these results together, our study identified a novel regulatory mechanism among SNRPA, miR-625-5p, circSEC62 and the NOTCH1/Snail pathway in HCC, which promoted metastasis of HCC and may provide effective suggestions for improving the prognosis of HCC patients with metastasis.
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Affiliation(s)
- Zhaohong Mo
- Fifth Department of General Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Ruixi Li
- Department of Hepatobiliary and Pancreatic Surgery, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Chuanlin Cao
- Fifth Department of General Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Yanjie Li
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Shiyang Zheng
- Department of Head and Neck surgery, Cancer Center of Guangzhou Medical University, Guangzhou, China
| | - Runxin Wu
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Jinhua Xue
- Department of Physiology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, China
| | - Jingxiong Hu
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Hongyu Meng
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Hang Zhai
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Weiling Huang
- Department of Breast Oncology, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Fang Zheng
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Boxuan Zhou
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
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Hu Z, Li M, Huo Z, Chen L, Liu S, Deng K, Lu X, Chen S, Fu Y, Xu A. U1 snRNP proteins promote proximal alternative polyadenylation sites by directly interacting with 3' end processing core factors. J Mol Cell Biol 2022; 14:6694001. [PMID: 36073763 PMCID: PMC9926334 DOI: 10.1093/jmcb/mjac054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/14/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
In eukaryotic cells, both alternative splicing and alternative polyadenylation (APA) play essential roles in the gene regulation network. U1 small ribonucleoprotein particle (U1 snRNP) is a major component of spliceosome, and U1 snRNP complex can suppress proximal APA sites through crosstalking with 3' end processing factors. However, here we show that both knockdown and overexpression of SNRPA, SNRPC, SNRNP70, and SNRPD2, the U1 snRNP proteins, promote the usage of proximal APA sites at the transcriptome level. SNRNP70 can drive the phase transition of PABPN1 from droplet to aggregate, which may reduce the repressive effects of PABPN1 on the proximal APA sites. Additionally, SNRNP70 can also promote the proximal APA sites by recruiting CPSF6, suggesting that the function of CPSF6 on APA is related with other RNA-binding proteins and cell context-dependent. Consequently, these results reveal that, on the contrary to U1 snRNP complex, the free proteins of U1 snRNP complex can promote proximal APA sites through the interaction with 3' end processing machinery.
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Affiliation(s)
| | | | | | - Liutao Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, China
| | - Susu Liu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, China
| | - Ke Deng
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, China
| | - Xin Lu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, China
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, China
| | | | - Anlong Xu
- Correspondence to: Anlong Xu, E-mail:
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5
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Hatch ST, Smargon AA, Yeo GW. Engineered U1 snRNAs to modulate alternatively spliced exons. Methods 2022; 205:140-148. [PMID: 35764245 PMCID: PMC11185844 DOI: 10.1016/j.ymeth.2022.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/30/2022] [Accepted: 06/23/2022] [Indexed: 10/17/2022] Open
Abstract
Alternative splicing accounts for a considerable portion of transcriptomic diversity, as most protein-coding genes are spliced into multiple mRNA isoforms. However, errors in splicing patterns can give rise to mis-splicing with pathological consequences, such as the congenital diseases familial dysautonomia, Duchenne muscular dystrophy, and spinal muscular atrophy. Small nuclear RNA (snRNA) components of the U snRNP family have been proposed as a therapeutic modality for the treatment of mis-splicing. U1 snRNAs offer great promise, with prior studies demonstrating in vivo efficacy, suggesting additional preclinical development is merited. Improvements in enabling technologies, including screening methodologies, gene delivery vectors, and relevant considerations from gene editing approaches justify further advancement of U1 snRNA as a therapeutic and research tool. With the goal of providing a user-friendly protocol, we compile and demonstrate a methodological toolkit for sequence-specific targeted perturbation of alternatively spliced pre-mRNA with engineered U1 snRNAs. We observe robust modulation of endogenous pre-mRNA transcripts targeted in two contrasting splicing contexts, SMN2 exon 7 and FAS exon 6, exhibiting the utility and applicability of engineered U1 snRNA to both inclusion and exclusion of targeted exons. We anticipate that these demonstrations will contribute to the usability of U1 snRNA in investigating splicing modulation in eukaryotic cells, increasing accessibility to the broader research community.
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Affiliation(s)
- Samuel T Hatch
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, La Jolla, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Aaron A Smargon
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, La Jolla, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, La Jolla, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA.
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6
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Covello G, Ibrahim GH, Bacchi N, Casarosa S, Denti MA. Exon Skipping Through Chimeric Antisense U1 snRNAs to Correct Retinitis Pigmentosa GTPase-Regulator ( RPGR) Splice Defect. Nucleic Acid Ther 2022; 32:333-349. [PMID: 35166581 PMCID: PMC9416563 DOI: 10.1089/nat.2021.0053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Inherited retinal dystrophies are caused by mutations in more than 250 genes, each of them carrying several types of mutations that can lead to different clinical phenotypes. Mutations in Retinitis Pigmentosa GTPase-Regulator (RPGR) cause X-linked Retinitis pigmentosa (RP). A nucleotide substitution in intron 9 of RPGR causes the increase of an alternatively spliced isoform of the mature mRNA, bearing exon 9a (E9a). This introduces a stop codon, leading to truncation of the protein. Aiming at restoring impaired gene expression, we developed an antisense RNA-based therapeutic approach for the skipping of RPGR E9a. We designed a set of specific U1 antisense snRNAs (U1_asRNAs) and tested their efficacy in vitro, upon transient cotransfection with RPGR minigene reporter systems in HEK-293T, 661W, and PC-12 cell lines.
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Affiliation(s)
- Giuseppina Covello
- RNA Biology and Biotechnology Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Gehan H Ibrahim
- Department of Medical Biochemistry, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Niccolò Bacchi
- RNA Biology and Biotechnology Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Simona Casarosa
- Neural Development and Regeneration Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy.,Centre for Medical Science - CIS Med, University of Trento, Trento, Italy.,CNR Neuroscience Institute, Pisa, Italy
| | - Michela Alessandra Denti
- RNA Biology and Biotechnology Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy.,CNR Neuroscience Institute, Pisa, Italy
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7
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The upstream 5' splice site remains associated to the transcription machinery during intron synthesis. Nat Commun 2021; 12:4545. [PMID: 34315864 PMCID: PMC8316553 DOI: 10.1038/s41467-021-24774-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/02/2021] [Indexed: 12/28/2022] Open
Abstract
In the earliest step of spliceosome assembly, the two splice sites flanking an intron are brought into proximity by U1 snRNP and U2AF along with other proteins. The mechanism that facilitates this intron looping is poorly understood. Using a CRISPR interference-based approach to halt RNA polymerase II transcription in the middle of introns in human cells, we discovered that the nascent 5′ splice site base pairs with a U1 snRNA that is tethered to RNA polymerase II during intron synthesis. This association functionally corresponds with splicing outcome, involves bona fide 5′ splice sites and cryptic intronic sites, and occurs transcriptome-wide. Overall, our findings reveal that the upstream 5′ splice sites remain attached to the transcriptional machinery during intron synthesis and are thus brought into proximity of the 3′ splice sites; potentially mediating the rapid splicing of long introns. We know that most splicing reactions take place co-transcriptionally, but how the transcription machinery facilitate splicing of introns is unknown. Here the authors show that the 5′ splice site remains associated with the transcription machinery during intron synthesis through U1 snRNP, providing a basis for the rapid splicing reaction of introns.
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8
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Cheng Z, Shang Y, Xu X, Dong Z, Zhang Y, Du Z, Lu X, Zhang T. Presenilin 1 mutation likely contributes to U1 small nuclear RNA dysregulation and Alzheimer's disease-like symptoms. Neurobiol Aging 2021; 100:1-10. [PMID: 33450722 DOI: 10.1016/j.neurobiolaging.2020.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 12/10/2020] [Accepted: 12/13/2020] [Indexed: 12/15/2022]
Abstract
Previous studies showed that U1 small nuclear RNA (snRNA) was selectively enriched in the brain of individuals with familial Alzheimer's disease (AD), resulting in widespread changes in RNA splicing. Our study further reported that presenilin-1 (PSEN1) induced an increase in U1 snRNA expression, accompanied by changed amyloid precursor protein expression, β-amyloid level, and cell death in SH-SY5Y cells. However, the effect of U1 snRNA overexpression on learning and memory is still unclear. In the present study, we found that neuronal U1 snRNA overexpression could generate U1 snRNA aggregates in the nuclear, accompanied by the widespread alteration of RNA splicing, resulting in the impairments of synaptic plasticity and spatial memory. In addition, more U1 snRNAs is bound to the intron binding sites accompanied by an increased intracellular U1 snRNA level. This suggests that U1 snRNA overexpression regulates RNA splicing and gene expression in neurons by manipulating the recruitment of the U1 snRNA to the nascent transcripts. Using in situ hybridization staining of human central nervous system-type neurons, we identified nuclear aggregates of U1 snRNA in neurons by upregulating the U1 snRNA level. Quantitative polymerase chain reaction analysis showed U1 snRNA accumulation in the insoluble fraction of neurons with PSEN1 mutation neurons rather than other types of U snRNAs. These results show an independent function of U1 snRNA in regulating RNA splicing, suggesting that aberrant RNA processing may mediate neurodegeneration induced by PSEN1 mutation.
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Affiliation(s)
- Zhi Cheng
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China
| | - Yingchun Shang
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China
| | - Xinxin Xu
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China
| | - Zhiqiang Dong
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China
| | - Yongwang Zhang
- College of Pharmacy, Nankai University, Tianjin, PR China
| | - Zhanqiang Du
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China
| | - Xinyi Lu
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China; College of Pharmacy, Nankai University, Tianjin, PR China
| | - Tao Zhang
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China.
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9
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Abstract
U1 snRNP is one of the most abundant ribonucleoprotein (RNP) complexes in eukaryotic cells and is estimated to be approximately 1 million copies per cell. Apart from its canonical role in mRNA splicing, this complex has emerged as a key regulator of eukaryotic mRNA length via inhibition of mRNA 3'-end processing at numerous intronic polyadenylation sites, in a process that is also termed 'U1 snRNP telescripting'. Several reviews have extensively described the concept of U1 telescripting and subsequently highlighted its potential impacts in mRNA metabolism. Here, we review what is currently known regarding the underlying mechanisms of this important phenomenon and discuss open questions and future challenges.
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Affiliation(s)
- Yi Ran
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Yanhui Deng
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Chengguo Yao
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, China.,Department of Genetics and Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
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10
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Noncoding RNAs Set the Stage for RNA Polymerase II Transcription. Trends Genet 2020; 37:279-291. [PMID: 33046273 DOI: 10.1016/j.tig.2020.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/24/2022]
Abstract
Effective synthesis of mammalian messenger (m)RNAs depends on many factors that together direct RNA polymerase II (pol II) through the different stages of the transcription cycle and ensure efficient cotranscriptional processing of mRNAs. In addition to the many proteins involved in transcription initiation, elongation, and termination, several noncoding (nc)RNAs also function as global transcriptional regulators. Understanding the mode of action of these non-protein regulators has been an intense area of research in recent years. Here, we describe how these ncRNAs influence key regulatory steps of the transcription process, to affect large numbers of genes. Through direct association with pol II or by modulating the activity of transcription or RNA processing factors, these regulatory RNAs perform critical roles in gene expression.
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11
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5' and 3' splicing signals evolution in vertebrates: Analysis in a conserved gene family. Comput Biol Chem 2020; 86:107251. [PMID: 32224443 DOI: 10.1016/j.compbiolchem.2020.107251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 03/08/2020] [Accepted: 03/13/2020] [Indexed: 01/09/2023]
Abstract
The mitochondrial solute carrier genes (SLC25) are highly conserved during vertebrate evolution. In most SLC25 genes of zebrafish, chicken, mouse, and human, the introns are located at exactly superimposable positions. In these topographically corresponding introns we studied the composition of the initial and terminal hexanucleotides (5'ss and 3'ss) which are instrumental in splicing signaling, focusing on the evolutionary conservation/mutation dynamics of these genetically related sequences. At each position, the per cent conservation of zebrafish individual nucleotides in chicken, mouse and human is proportional to their percent frequency in zebrafish; furthermore, nucleotide mutations are biased in favor of the more represented nucleotides, thus compensating for those highly represented zebrafish nucleotides which have not been conserved. As a result of these evolutionary dynamics, the general nucleotide composition at each position has remained relatively conserved throughout vertebrates. At 5'ss, following the canonical GT, A and G are largely prevailing at position +3, A at +4 and G at +5 (GT[A/G]AGx). At 3'ss, T and C are largely prevailing at positions -6, -5 and -3, preceding the canonical intron terminal AG ([C/T] [C/T]x[C/T]AG). However, the actual composition of the tetranucleotides at 5' and 3' often does not conform to the above scheme. At 5'ss the more canonical sequence is completely expressed in 63% of cases and partially (2 or 1 matches) in 37 % of cases. At 3'ss the more canonical sequence is completely expressed in 71 % of cases and partially (2 or 1 matches) in 29 % of cases. The nucleotide conservation loss (nucleotide mutation) is higher in the evolution from fish to the last common ancestor of birds and mammals (58 %), then diminishes in the successive evolution steps up to the mammalian common ancestor (10 %), and becomes still lower at the divergence of rodents and primates (5 %).
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12
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Coutinho MF, Matos L, Santos JI, Alves S. RNA Therapeutics: How Far Have We Gone? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:133-177. [PMID: 31342441 DOI: 10.1007/978-3-030-19966-1_7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In recent years, the RNA molecule became one of the most promising targets for therapeutic intervention. Currently, a large number of RNA-based therapeutics are being investigated both at the basic research level and in late-stage clinical trials. Some of them are even already approved for treatment. RNA-based approaches can act at pre-mRNA level (by splicing modulation/correction using antisense oligonucleotides or U1snRNA vectors), at mRNA level (inhibiting gene expression by siRNAs and antisense oligonucleotides) or at DNA level (by editing mutated sequences through the use of CRISPR/Cas). Other RNA approaches include the delivery of in vitro transcribed (IVT) mRNA or the use of oligonucleotides aptamers. Here we review these approaches and their translation into clinics trying to give a brief overview also on the difficulties to its application as well as the research that is being done to overcome them.
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Affiliation(s)
- Maria Francisca Coutinho
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal
| | - Liliana Matos
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal
| | - Juliana Inês Santos
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal
| | - Sandra Alves
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal.
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13
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Singh RN, Singh NN. A novel role of U1 snRNP: Splice site selection from a distance. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:634-642. [PMID: 31042550 DOI: 10.1016/j.bbagrm.2019.04.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 12/23/2022]
Abstract
Removal of introns by pre-mRNA splicing is fundamental to gene function in eukaryotes. However, understanding the mechanism by which exon-intron boundaries are defined remains a challenging endeavor. Published reports support that the recruitment of U1 snRNP at the 5'ss marked by GU dinucleotides defines the 5'ss as well as facilitates 3'ss recognition through cross-exon interactions. However, exceptions to this rule exist as U1 snRNP recruited away from the 5'ss retains the capability to define the splice site, where the cleavage takes place. Independent reports employing exon 7 of Survival Motor Neuron (SMN) genes suggest a long-distance effect of U1 snRNP on splice site selection upon U1 snRNP recruitment at target sequences with or without GU dinucleotides. These findings underscore that sequences distinct from the 5'ss may also impact exon definition if U1 snRNP is recruited to them through partial complementarity with the U1 snRNA. In this review we discuss the expanded role of U1 snRNP in splice-site selection due to U1 ability to be recruited at more sites than predicted solely based on GU dinucleotides.
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Affiliation(s)
- Ravindra N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States of America.
| | - Natalia N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States of America
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14
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Guiro J, Murphy S. Regulation of expression of human RNA polymerase II-transcribed snRNA genes. Open Biol 2018; 7:rsob.170073. [PMID: 28615474 PMCID: PMC5493778 DOI: 10.1098/rsob.170073] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/11/2017] [Indexed: 12/31/2022] Open
Abstract
In addition to protein-coding genes, RNA polymerase II (pol II) transcribes numerous genes for non-coding RNAs, including the small-nuclear (sn)RNA genes. snRNAs are an important class of non-coding RNAs, several of which are involved in pre-mRNA splicing. The molecular mechanisms underlying expression of human pol II-transcribed snRNA genes are less well characterized than for protein-coding genes and there are important differences in expression of these two gene types. Here, we review the DNA features and proteins required for efficient transcription of snRNA genes and co-transcriptional 3′ end formation of the transcripts.
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Affiliation(s)
- Joana Guiro
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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15
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Pokorná P, Kruse H, Krepl M, Šponer J. QM/MM Calculations on Protein-RNA Complexes: Understanding Limitations of Classical MD Simulations and Search for Reliable Cost-Effective QM Methods. J Chem Theory Comput 2018; 14:5419-5433. [PMID: 30199638 DOI: 10.1021/acs.jctc.8b00670] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although atomistic explicit-solvent Molecular Dynamics (MD) is a popular tool to study protein-RNA recognition, satisfactory MD description of protein-RNA complexes is not always achieved. Unfortunately, it is often difficult to separate MD simulation instabilities primarily caused by the simple point-charge molecular mechanics (MM) force fields from problems related to the notorious uncertainties in the starting structures. Herein, we report a series of large-scale QM/MM calculations on the U1A protein-RNA complex. This experimentally well-characterized system has an intricate protein-RNA interface, which is very unstable in MD simulations. The QM/MM calculations identify several H-bonds poorly described by the MM method and thus indicate the sources of instabilities of the U1A interface in MD simulations. The results suggest that advanced QM/MM computations could be used to indirectly rationalize problems seen in MM-based MD simulations of protein-RNA complexes. As the most accurate QM method, we employ the computationally demanding meta-GGA density functional TPSS-D3(BJ)/def2-TZVP level of theory. Because considerably faster methods would be needed to extend sampling and to study even larger protein-RNA interfaces, a set of low-cost QM/MM methods is compared to the TPSS-D3(BJ)/def2-TZVP data. The PBEh-3c and B97-3c density functional composite methods appear to be suitable for protein-RNA interfaces. In contrast, HF-3c and the tight-binding Hamiltonians DFTB3-D3 and GFN-xTB perform unsatisfactorily and do not provide any advantage over the MM description. These conclusions are supported also by similar analysis of a simple HutP protein-RNA interface, which is well-described by MD with the exception of just one H-bond. Some other methodological aspects of QM/MM calculations on protein-RNA interfaces are discussed.
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Affiliation(s)
- Pavlína Pokorná
- Institute of Biophysics of the Czech Academy of Sciences , Královopolská 135 , Brno 612 65 , Czech Republic
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences , Královopolská 135 , Brno 612 65 , Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences , Královopolská 135 , Brno 612 65 , Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Královopolská 135 , Brno 612 65 , Czech Republic.,CEITEC - Central European Institute of Technology, Masaryk University , Campus Bohunice, Kamenice 5 , Brno 625 00 , Czech Republic
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16
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Dou N, Yang D, Yu S, Wu B, Gao Y, Li Y. SNRPA enhances tumour cell growth in gastric cancer through modulating NGF expression. Cell Prolif 2018; 51:e12484. [PMID: 30039889 DOI: 10.1111/cpr.12484] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/22/2018] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVES SNRPA is a protein component of U1 small nuclear ribonucleoprotein (U1 snRNP) complex, which takes part in the splicing of pre-mRNAs. Its expression and function in tumour remain unknown. Herein, we elucidated the functional contribution of SNRPA to the progression of gastric cancer (GC). MATERIALS AND METHODS SNRPA expression was investigated in a GC tissue microarray by immunohistochemical staining. Cell proliferation was evaluated by CCK-8, colony formation and EdU incorporation assays. A mouse xenograft model was used to detect the tumourigenicity. Gene expression profiling was performed and then the potential target genes were verified by quantitative real-time PCR and western blot analyses. The functional relevance between SNRPA and its target gene was examined by cell growth assays. RESULTS SNRPA expression was higher in tumour tissues than in matched normal gastric mucosa tissues, and it was positively correlated with the tumour size and progression. High SNRPA expression indicated poor prognosis of GC patients. Silencing SNRPA in GC cells markedly inhibited cell proliferation in vitro and tumour growth in a xenograft model, while overexpressing SNRPA exhibited opposite results. Moreover, we identified NGF (Nerve growth factor) as a downstream effector of SNRPA and further proved that NGF was crucial for SNRPA-mediated GC cell growth. CONCLUSIONS These findings suggested that SNRPA may contribute to GC progression via NGF and could be a prognostic biomarker for GC.
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Affiliation(s)
- Ning Dou
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Dong Yang
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shijun Yu
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Binghao Wu
- Harvard Medical School, Massachusetts General Hospital, Cutaneous Biology Research Center, Charlestown, MA, USA
| | - Yong Gao
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yandong Li
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Shanghai East Hospital, Research Center for Translational Medicine, Tongji University School of Medicine, Shanghai, China
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17
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Cheng Z, Sun Y, Niu X, Shang Y, Ruan J, Chen Z, Gao S, Zhang T. Gene expression profiling reveals U1 snRNA regulates cancer gene expression. Oncotarget 2017; 8:112867-112874. [PMID: 29348872 PMCID: PMC5762557 DOI: 10.18632/oncotarget.22842] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/10/2017] [Indexed: 11/25/2022] Open
Abstract
U1 small nuclear RNA (U1 snRNA), as one of the most abundant ncRNAs in human cells, plays an important role in splicing of pre-mRNAs. Compared to previous studies which have focused on the primary function of U1 snRNA and the neurodegenerative diseases caused by abnormalities of U1 snRNA, this study is to investigate how U1 snRNA over-expression affects the expression of mammal genes on a genome-wide scale. By comparing the gene expression profiles of U1 snRNA over-expressed cells with those of their controls using microarray experiments, 916 genes or loci were identified significantly Differentially Expressed (DE). These 595 up-regulated DE genes and 321 down-regulated DE genes were analyzed using annotations from GO categories and pathways from the KEGG database. As a result, three of 12 enriched pathways were well-known cancer pathways, while the other nine pathways were associated to cancers in previous studies. The further analysis of 73 genes involved in 12 pathways suggested that U1 snRNA could regulate cancer gene expression. The microarray data under the GEO Series accession number GSE84304 is available in the NCBI GEO database.
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Affiliation(s)
- Zhi Cheng
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, P.R. China
- State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu 730046, P.R. China
| | - Yu Sun
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, P.R. China
- Institute of Statistics, Nankai University, Tianjin 300071, P.R. China
| | - Xiaoran Niu
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, P.R. China
| | - Yingchun Shang
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, P.R. China
| | - Jishou Ruan
- School of Mathematical Sciences, Nankai University, Tianjin 300071, P.R. China
| | - Ze Chen
- State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu 730046, P.R. China
| | - Shan Gao
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, P.R. China
- Institute of Statistics, Nankai University, Tianjin 300071, P.R. China
| | - Tao Zhang
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, P.R. China
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18
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Cheng Z, Shang Y, Gao S, Zhang T. Overexpression of U1 snRNA induces decrease of U1 spliceosome function associated with Alzheimer's disease. J Neurogenet 2017; 31:337-343. [PMID: 29098922 DOI: 10.1080/01677063.2017.1395425] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We recently reported that presenilin-1 (PS1) induced an increase of U1 snRNA expression accompanied with the change of amyloid precursor protein expression, β-amyloid level and cell death. In the present study, our data showed that both overexpression and knockdown of U1 snRNA could cause the loss in the function of U1 snRNA and resulted in PCPA as well as the same downstream phenomena including the expression changes of genes specific to AD, tau hyperphosphorylation on the site of Thr212, the decrease of acetylated α-tubulin, the reduction of cell viability and upregulation of RIPK1, RIPK3 and caspase8. These findings not only helped researchers better understand the functions of U1 snRNA, but also paved the way to reveal the mechanisms of AD from a different point of view and may find a new therapeutic target for the disease.
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Affiliation(s)
- Zhi Cheng
- a College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education , Nankai University , Tianjin , PR China
| | - Yingchun Shang
- a College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education , Nankai University , Tianjin , PR China
| | - Shan Gao
- a College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education , Nankai University , Tianjin , PR China
| | - Tao Zhang
- a College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education , Nankai University , Tianjin , PR China
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19
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Shaul O. How introns enhance gene expression. Int J Biochem Cell Biol 2017; 91:145-155. [PMID: 28673892 DOI: 10.1016/j.biocel.2017.06.016] [Citation(s) in RCA: 231] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 06/26/2017] [Accepted: 06/30/2017] [Indexed: 01/18/2023]
Abstract
In many eukaryotes, including mammals, plants, yeast, and insects, introns can increase gene expression without functioning as a binding site for transcription factors. This phenomenon was termed 'intron-mediated enhancement'. Introns can increase transcript levels by affecting the rate of transcription, nuclear export, and transcript stability. Moreover, introns can also increase the efficiency of mRNA translation. This review discusses the current knowledge about these processes. The role of splicing in IME and the significance of intron position relative to the sites of transcription and translation initiation are elaborated. Particular emphasis is placed on the question why different introns, present at the same location of the same genes and spliced at a similar high efficiency, can have very different impacts on expression - from almost no effect to considerable stimulation. This situation can be at least partly accounted for by the identification of splicing-unrelated intronic elements with a special ability to enhance mRNA accumulation or translational efficiency. The many factors that could lead to the large variation observed between the impact of introns in different genes and experimental systems are highlighted. It is suggested that there is no sole, definite answer to the question "how do introns enhance gene expression". Rather, each intron-gene combination might undergo its own unique mixture of processes that lead to the perceptible outcome.
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Affiliation(s)
- Orit Shaul
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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20
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Vazquez-Arango P, Vowles J, Browne C, Hartfield E, Fernandes H, Mandefro B, Sareen D, James W, Wade-Martins R, Cowley SA, Murphy S, O'Reilly D. Variant U1 snRNAs are implicated in human pluripotent stem cell maintenance and neuromuscular disease. Nucleic Acids Res 2016; 44:10960-10973. [PMID: 27536002 PMCID: PMC5159530 DOI: 10.1093/nar/gkw711] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 08/01/2016] [Accepted: 08/04/2016] [Indexed: 02/06/2023] Open
Abstract
The U1 small nuclear (sn)RNA (U1) is a multifunctional ncRNA, known for its pivotal role in pre-mRNA splicing and regulation of RNA 3' end processing events. We recently demonstrated that a new class of human U1-like snRNAs, the variant (v)U1 snRNAs (vU1s), also participate in pre-mRNA processing events. In this study, we show that several human vU1 genes are specifically upregulated in stem cells and participate in the regulation of cell fate decisions. Significantly, ectopic expression of vU1 genes in human skin fibroblasts leads to increases in levels of key pluripotent stem cell mRNA markers, including NANOG and SOX2. These results reveal an important role for vU1s in the control of key regulatory networks orchestrating the transitions between stem cell maintenance and differentiation. Moreover, vU1 expression varies inversely with U1 expression during differentiation and cell re-programming and this pattern of expression is specifically de-regulated in iPSC-derived motor neurons from Spinal Muscular Atrophy (SMA) type 1 patient's. Accordingly, we suggest that an imbalance in the vU1/U1 ratio, rather than an overall reduction in Uridyl-rich (U)-snRNAs, may contribute to the specific neuromuscular disease phenotype associated with SMA.
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Affiliation(s)
- Pilar Vazquez-Arango
- University of Oxford, Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK
| | - Jane Vowles
- University of Oxford, Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK,Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
| | - Cathy Browne
- University of Oxford, Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK
| | - Elizabeth Hartfield
- Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK,Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Hugo J. R. Fernandes
- Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK,Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Berhan Mandefro
- Cedars-Sinai Medical Center, Board of Governors-Regenerative Medicine Institute and Department of Biomedical Sciences, 8700 Beverly Blvd, AHSP A8418, Los Angeles, CA 90048, USA,iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Dhruv Sareen
- Cedars-Sinai Medical Center, Board of Governors-Regenerative Medicine Institute and Department of Biomedical Sciences, 8700 Beverly Blvd, AHSP A8418, Los Angeles, CA 90048, USA,iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - William James
- University of Oxford, Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK
| | - Richard Wade-Martins
- Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK,Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Sally A. Cowley
- University of Oxford, Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK,Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
| | - Shona Murphy
- University of Oxford, Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK
| | - Dawn O'Reilly
- University of Oxford, Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK
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21
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Double-target Antisense U1snRNAs Correct Mis-splicing Due to c.639+861C>T and c.639+919G>A GLA Deep Intronic Mutations. MOLECULAR THERAPY-NUCLEIC ACIDS 2016; 5:e380. [PMID: 27779620 PMCID: PMC5095687 DOI: 10.1038/mtna.2016.88] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 08/22/2016] [Indexed: 12/26/2022]
Abstract
Fabry disease is a rare X-linked lysosomal storage disorder caused by deficiency of the α-galactosidase A (α-Gal A) enzyme, which is encoded by the GLA gene. GLA transcription in humans produces a major mRNA encoding α-Gal A and a minor mRNA of unknown function, which retains a 57-nucleotide-long cryptic exon between exons 4 and 5, bearing a premature termination codon. NM_000169.2:c.639+861C>T and NM_000169.2:c.639+919G>A GLA deep intronic mutations have been described to cause Fabry disease by inducing overexpression of the alternatively spliced mRNA, along with a dramatic decrease in the major one. Here, we built a wild-type GLA minigene and two minigenes that carry mutations c.639+861C>T and c.639+919G>A. Once transfected into cells, the minigenes recapitulate the molecular patterns observed in patients, at the mRNA, protein, and enzymatic level. We constructed a set of specific double-target U1asRNAs to correct c.639+861C>T and c.639+919G>A GLA mutations. Efficacy of U1asRNAs in inducing the skipping of the cryptic exon was evaluated upon their transient co-transfection with the minigenes in COS-1 cells, by real-time polymerase chain reaction (PCR), western blot analysis, and α-Gal A enzyme assay. We identified a set of U1asRNAs that efficiently restored α-Gal A enzyme activity and the correct splicing pathways in reporter minigenes. We also identified a unique U1asRNA correcting both mutations as efficently as the mutation-specific U1asRNAs. Our study proves that an exon skipping-based approach recovering α-Gal A activity in the c.639+861C>T and c.639+919G>A GLA mutations is active.
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22
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Mayne BT, Bianco-Miotto T, Buckberry S, Breen J, Clifton V, Shoubridge C, Roberts CT. Large Scale Gene Expression Meta-Analysis Reveals Tissue-Specific, Sex-Biased Gene Expression in Humans. Front Genet 2016; 7:183. [PMID: 27790248 PMCID: PMC5062749 DOI: 10.3389/fgene.2016.00183] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/27/2016] [Indexed: 12/29/2022] Open
Abstract
The severity and prevalence of many diseases are known to differ between the sexes. Organ specific sex-biased gene expression may underpin these and other sexually dimorphic traits. To further our understanding of sex differences in transcriptional regulation, we performed meta-analyses of sex biased gene expression in multiple human tissues. We analyzed 22 publicly available human gene expression microarray data sets including over 2500 samples from 15 different tissues and 9 different organs. Briefly, by using an inverse-variance method we determined the effect size difference of gene expression between males and females. We found the greatest sex differences in gene expression in the brain, specifically in the anterior cingulate cortex, (1818 genes), followed by the heart (375 genes), kidney (224 genes), colon (218 genes), and thyroid (163 genes). More interestingly, we found different parts of the brain with varying numbers and identity of sex-biased genes, indicating that specific cortical regions may influence sexually dimorphic traits. The majority of sex-biased genes in other tissues such as the bladder, liver, lungs, and pancreas were on the sex chromosomes or involved in sex hormone production. On average in each tissue, 32% of autosomal genes that were expressed in a sex-biased fashion contained androgen or estrogen hormone response elements. Interestingly, across all tissues, we found approximately two-thirds of autosomal genes that were sex-biased were not under direct influence of sex hormones. To our knowledge this is the largest analysis of sex-biased gene expression in human tissues to date. We identified many sex-biased genes that were not under the direct influence of sex chromosome genes or sex hormones. These may provide targets for future development of sex-specific treatments for diseases.
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Affiliation(s)
- Benjamin T Mayne
- Robinson Research Institute, University of AdelaideAdelaide, SA, Australia; Adelaide Medical School, University of AdelaideAdelaide, SA, Australia
| | - Tina Bianco-Miotto
- Robinson Research Institute, University of AdelaideAdelaide, SA, Australia; School of Agriculture, Food and Wine, Waite Research Institute, University of AdelaideAdelaide, SA, Australia
| | - Sam Buckberry
- Harry Perkins Institute of Medical Research, The University of Western AustraliaPerth, WA, Australia; Plant Energy Biology, Australian Research Council Centre of Excellence, The University of Western AustraliaPerth, WA, Australia
| | - James Breen
- Robinson Research Institute, University of AdelaideAdelaide, SA, Australia; Bioinformatics Hub, School of Biological Sciences, University of AdelaideAdelaide, SA, Australia
| | - Vicki Clifton
- Mater Research Institute, University of Queensland Brisbane, QLD, Australia
| | - Cheryl Shoubridge
- Robinson Research Institute, University of AdelaideAdelaide, SA, Australia; Adelaide Medical School, University of AdelaideAdelaide, SA, Australia
| | - Claire T Roberts
- Robinson Research Institute, University of AdelaideAdelaide, SA, Australia; Adelaide Medical School, University of AdelaideAdelaide, SA, Australia
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